R Notebook

library(GOplot)

Loading required package: ggplot2
Loading required package: ggdendro
Loading required package: gridExtra
Loading required package: RColorBrewer

name <- 'heatmap_logFC0.3_ncluster6'
folder <- paste('../tables/BEAM/', name, sep='')
gsea_files <- list.files(paste(folder, '/REVIGO_cleaned/', sep=''))
clusters <- c(1,2,3,4,6)
gsea <- list()
genelist <- list()
for (i in clusters){
  gsea_cluster <- read.table(paste(folder, '/REVIGO_cleaned/', 'REVIGO_cluster', i, '_cleaned.tsv', sep=''), header=T)
  gsea_cluster['cluster'] <- i
  genes_cluster <- read.table(paste(folder, '/genelist_cluster', i, '.tsv', sep=''))
  gsea[[i]] <- gsea_cluster
  genelist[[i]] <- genes_cluster
}
gsea <- do.call("rbind", gsea)
genelist <- do.call("rbind", genelist)

create_terms <- function(gsea){
  return(data.frame(category=gsea$gsea.domain, ID=gsea$revigo.term_ID, term=gsea$revigo.description, adj_pval=gsea$gsea.p.value, genes=gsea$gsea.intersection, cluster=gsea$cluster))
}
create_genes <- function(genelist){
  return(data.frame(ID=genelist$gene_short_name, logFC=genelist$avgLogFC_State2_State3))
}
#genes_c2_swapped <- data.frame(ID=genes_c2$ID, logFC=genes_c2$logFC*-1)

All terms

terms <- create_terms(gsea)
genes <- create_genes(genelist)
circ <- circle_dat(terms, genes)

Terms associated with metabolic branch

#genes <- rbind(genes_c2_swapped, genes_c5_swapped, genes_c4_swapped)
circ_metabolic <- circle_dat(terms_metabolic, genes)

Error in is.data.frame(x) : object 'terms_metabolic' not found

Terms associated with ECM branch

circ_metabolic <- circle_dat(terms_metabolic, genes_swapped)

Error in toupper(genes$ID) : object 'genes_swapped' not found

Only upregulated terms

gsea_upregulated <- gsea[gsea$cluster %in% c(2,6,3),]
terms_upregulated <- create_terms(gsea_upregulated)
circ_upregulated <- circle_dat(terms_upregulated, genes)

GOBar(circ_upregulated)

GOBubble(subset(circ_upregulated, category=='CC'), labels=2, ID=F, colour=c('#ff8284', '#ff8284', '#ff8284'))